BACKGROUND: Circadian clocks provide an adaptive advantage through anticipation of daily and seasonal environmental
changes. In plants, the central clock oscillator is regulated by several interlocking feedback loops. It was shown that a
substantial proportion of the Arabidopsis genome cycles with phases of peak expression covering the entire day.
Synchronized...
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and cis-Regulatory Modules
SergeiA. Filichkin1, Ghislain Breton2¤a, Henry D. Priest1, Palitha
BACKGROUND: Circadian clocks provide an adaptive advantage through anticipation of daily and seasonal environmental
changes. In plants, the central clock oscillator is regulated by several interlocking feedback loops. It was shown that a
substantial proportion of the Arabidopsis genome cycles with phases of peak expression covering the entire day.
Synchronized...
Plants possess two myosin classes, VIII and XI. The myosins XI are implicated in organelle transport, filamentous actin
organization, and cell and plant growth. Due to the large size of myosin gene families, knowledge of these molecular motors
remains patchy. Using deep transcriptome sequencing and bioinformatics, we systematically investigated myosin...
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, SergeiA. Filichkin, Samuel E. Fox, Pankaj Jaiswal, Kira S. Makarova,
Eugene V. Koonin, and Valerian V
Plants possess two myosin classes, VIII and XI. The myosins XI are implicated in organelle transport, filamentous actin
organization, and cell and plant growth. Due to the large size of myosin gene families, knowledge of these molecular motors
remains patchy. Using deep transcriptome sequencing and bioinformatics, we systematically investigated myosin...
One-electron oxidation of the μ-oxo dimer
(cis,cis-[Ruᴵᴵᴵ(bpy)₂(OH₂)]₂O⁴⁺, {3,3}) to {3,4} by S₂O₈²⁻ can
be described by three concurrent reaction pathways corresponding
to the three protic forms of {3,3}. Free energy
correlations of the rate constants, transient species dynamics
determined by pulse radiolysis, and medium and temperature
dependencies of the alkaline...
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(bpy)2(OH2)]2O4+ “Blue Dimer”
James K. Hurst,† Margo Roemeling,‡ and Sergei V. Lymar
One-electron oxidation of the μ-oxo dimer
(cis,cis-[Ruᴵᴵᴵ(bpy)₂(OH₂)]₂O⁴⁺, {3,3}) to {3,4} by S₂O₈²⁻ can
be described by three concurrent reaction pathways corresponding
to the three protic forms of {3,3}. Free energy
correlations of the rate constants, transient species dynamics
determined by pulse radiolysis, and medium and temperature
dependencies of the alkaline...
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-[Ru(bpy)2(OH2)]2O
4+ “Blue Dimer”
James K. Hurst,† Margo D. Roemeling,‡ and Sergei V. Lymar
Barley (Hordeum vulgare) is an important component of heart-healthy
whole grain diets because it contains β-glucan. All current US barley
varieties with high β-glucan are spring habit and have waxy starch. Winter
varieties have agronomic advantages but require low-temperature tolerance
(LTT). Vernalization sensitivity (VS) is associated with higher
levels of...
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. Cereal Chem. 79, 596—599.
Cuesta-Marcos, A., P. Szucs, T. J. Close, T. Filichkin, G. J. Muehlbauer,
K. P
Barley (Hordeum vulgare) is an important component of heart-healthy
whole grain diets because it contains β-glucan. All current US barley
varieties with high β-glucan are spring habit and have waxy starch. Winter
varieties have agronomic advantages but require low-temperature tolerance
(LTT). Vernalization sensitivity (VS) is associated with higher
levels of...
Collaboration is crucial when advancing in scientific research. One person cannot
study all aspects of a system. That is why it is important for the scientific community to
communicate with each other and stay updated on research being conducted in other labs
around the world. In my research, I was...
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simple difference. A principal component of winterhardiness is low temperature
tolerance. However, low
The genetic underpinnings associated with the earliest stages of plant and animal domestication have remained elusive. Because a genome-wide response to selection can take many generations, the earliest detectable changes associated with domestication may first manifest as heritable changes to global patterns of gene expression. Here, to test this hypothesis,...
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. Fox, S., Filichkin, S. & Mockler, T. in Plant Systems Biology. (ed. Belostotsky, D. A.
553 chap. 5 79
Chemical synthesis of oligonucleotides is a widely used tool in the field of biochemistry.
Several methods for gene synthesis have been introduced in the growing area of genomics.
In this paper, a novel method of constructing dsDNA is proposed. Short (28-mer) oligo fragments
from a library were assembled through successive...
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.
(TIF)
Acknowledgments
We would like to thank Dr. SergeiFilichkin, Department of Botany and Plant
• Premise of the study: The dramatic advances offered by modern DNA sequencers continue to redefine the limits of what can be accomplished in comparative plant biology. Even with recent achievements, however, plant genomes present obstacles that can make it difficult to execute large-scale population and phylogenetic studies on next-generation...
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et al. Acacia auriculiformis, A. mangium Illumina
2011 Wu et al. Taxus cuspidata Roche/454
2011
Vegetative propagation allows the amplification of selected genotypes for research,
breeding, and commercial planting. However, efficient in vitro regeneration and
genetic transformation remains a major obstacle to research and commercial
application in many plant species. Our aims are to improve knowledge of gene
regulatory circuits important to meristem organization, and...
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. SergeiFilichkin, and Dr. Renee Arias for their advice on my research.
Ms. Cathleen Ma, Megan Allen
Pseudomonas syringae is a phylogenetically diverse species of Gram-negative bacterial plant pathogens responsible for crop
diseases around the world. The HrpL sigma factor drives expression of the major P. syringae virulence regulon. HrpL controls
expression of the genes encoding the structural and functional components of the type III secretion system...
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Tatiana S. Mucyn1, Scott Yourstone1,2, Abigail L. Lind1¤, Surojit Biswas1, Marc T. Nishimura1,
David A
Gramene (http://www.gramene.org) is a curated
online resource for comparative functional
genomics in crops and model plant species, currently
hosting 27 fully and 10 partially sequenced
reference genomes in its build number 38. Its
strength derives from the application of a phylogenetic
framework for genome comparison and the
use of ontologies...
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BioMarts: a hub for data
retrieval across taxonomic space. Database, 2011, bar030.
29. Filichkin,S.A
This thesis consists of three manuscripts addressing separate components of barley breeding, plus an introduction and a conclusion summarizing the status of barley in the Pacific Northwest, plus the implications of the research presented in this thesis. In the first manuscript, a package written for the statistical software "R" that...
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a conclusion summarizing the status of barley
in the Pacific Northwest, plus the implications of
• Premise of the study: The dramatic advances offered by modern DNA sequencers continue to redefine the limits of what can be accomplished in comparative plant biology. Even with recent achievements, however, plant genomes present obstacles that can make it difficult to execute large-scale population and phylogenetic studies on next-generation...
Full Text:
community
(e.g., roots from soil) and obtain a nearly complete sample of
all nucleotides contained within
Barley (Hordeum vulgare L.) has been cultivated for human consumption for thousands of years. However, most North Americans do not consume barley on a regular basis. In the last decade, there has been a renewed interest in barley production for human consumption. A number of quality traits estimate nutritional value...
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, WA 98273; A. Cuesta-Marcos, A.S. Ross, S. 6
Fisk, T. Kongraksawech, and P.M. Hayes, Dep. of Crop
BACKGROUND: Triticum monococcum (2n) is a close ancestor of T. urartu, the A-genome progenitor of cultivated hexaploid
wheat, and is therefore a useful model for the study of components regulating photomorphogenesis in diploid wheat. In
order to develop genetic and genomic resources for such a study, we constructed genome-wide transcriptomes...
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monococcum
Samuel E. Fox1."¤a, Matthew Geniza1,2.", Mamatha Hanumappa1., Sushma Naithani1,3, Chris
Winter hardiness in barley (Hordeum vulgare) is a trait targeted by breeding programs in order to expand the potential area of adaptation of fall-sown cereals. Vernalization requirement is an important factor in winter hardiness. A vernalization requirement is an extended period of low temperature required for transition from the vegetative...
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. Szűcs, , K. Meszaros, T. Filichkin, P. M. Hayes, L. Lang, and Z.
Bedo. 2005. The VRN-H2 locus is a
The field performance of genetic containment technologies–considered important for
certain uses of transgenic trees in forestry–are poorly known. We tested the efficiency of a
barnase gene driven by the TA29 tapetum-dominant promoter for influencing growth rate and
inducing male-sterility in a field trial of transgenic hybrid poplar (Populus tremula x...
Understanding the mechanisms through which stem cells self-renew is important for the development of new therapies to repair and restore damaged tissue. This research explores possible mechanisms of telomere mimic action and seeks to validate a new assay for evaluating telomere binding antagonists and studying the effects of telomere binding...
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possible mechanisms of telomere mimic action and seeks to validate a new
assay for evaluating telomere
New sources of genetic diversity must be incorporated into plant breeding programs if they are to continue increasing grain
yield and quality, and tolerance to abiotic and biotic stresses. Germplasm collections provide a source of genetic and
phenotypic diversity, but characterization of these resources is required to increase their utility...
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-Amatriaín M, Cuesta-Marcos A, Endelman JB, Comadran J, Bonman JM,
et al. (2014) The USDA Barley Core
BACKGROUND:
Plant gametophytes play central roles in sexual reproduction. A hallmark of the plant life
cycle is that gene expression is required in the haploid gametophytes. Consequently, many
mutant phenotypes are expressed in this phase.
RESULTS:
We perform a quantitative RNA-seq analysis of embryo sacs, comparator ovules with the
embryo...
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gametophytic functions via RNA-seq
analysis of maize gametophytic transcriptomes
Chettoor, A. M., Givan, S. A
Black raspberry (Rubus occidentalis L.) is a high-value crop in the Pacific Northwest of North America with an international marketplace. Few genetic resources are readily available and little improvement has been achieved through breeding efforts to address production challenges involved in growing this crop. Contributing to its lack of improvement...
Global change and its associated temperature increase has directly or indirectly changed the distributions of hosts and
pathogens, and has affected host immunity, pathogen virulence and growth rates. This has resulted in increased disease in
natural plant and animal populations worldwide, including scleractinian corals. While the effects of temperature increase...
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Transcriptomic Remodeling, while Vibrio coralliilyticus Infection Induces a More Targeted Immuno-Suppression
Brachypodium distachyon is a close relative of many important cereal crops. Abiotic stress tolerance has a significant impact
on productivity of agriculturally important food and feedstock crops. Analysis of the transcriptome of Brachypodium after
chilling, high-salinity, drought, and heat stresses revealed diverse differential expression of many transcripts. Weighted Gene
Co-Expression...
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, Todd P. Michael4¤a,
Todd C. Mockler1,2,3*
1 Donald Danforth Plant Science Center, Saint Louis
Viruses are obligatory parasites that depend on host cellular factors for their replication as well as for their local and systemic
movement to establish infection. Although myosin motors are thought to contribute to plant virus infection, their exact roles
in the specific infection steps have not been addressed. Here we...
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Distinct Roles in Reproduction
and Transport of Tobacco Mosaic Virus
Khalid Amari 1¤a*, Martin Di Donato1¤b
In transboundary river basins, political borders oftentimes trace shared rivers across a basin. A border between territories can be seen as a space that is separated; however, it is actually one with the potential to unite populations and environments. A river basin is generally defined by its topography and hydrology....
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rivers across a
basin. A border between territories can be seen as a space that is separated; however